RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:26:31 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/2_msa/Q14999_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/3_mltree/Q14999.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647591 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/2_msa/Q14999_nogap_msa.fasta [00:00:00] Loaded alignment with 659 taxa and 1698 sites WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and sp_Q9WTX6_CUL1_MOUSE_10090 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_G1MRX7_G1MRX7_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_F6X2V7_F6X2V7_ORNAN_9258 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_B1WBY1_B1WBY1_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_G3SSB7_G3SSB7_LOXAF_9785 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_G3WZI9_G3WZI9_SARHA_9305 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_H0YU78_H0YU78_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A151P2L7_A0A151P2L7_ALLMI_8496 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A1S3FMP4_A0A1S3FMP4_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A1U8D295_A0A1U8D295_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A1V4JV91_A0A1V4JV91_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A218UAV5_A0A218UAV5_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1D5P2L3_A0A1D5P2L3_CHICK_9031 and tr_A0A2Y9DW63_A0A2Y9DW63_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and sp_Q5R4G6_CUL1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_G2HEC7_G2HEC7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_H0XBT6_H0XBT6_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and sp_Q13616_CUL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_U3CZT1_U3CZT1_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A096N574_A0A096N574_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A0D9R3Z4_A0A0D9R3Z4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A1U7T682_A0A1U7T682_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A2K5NGS0_A0A2K5NGS0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A2K6CHS8_A0A2K6CHS8_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A2K6AL87_A0A2K6AL87_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QTR6_G1QTR6_NOMLE_61853 and tr_A0A2R9C048_A0A2R9C048_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QGP7_G3QGP7_GORGO_9595 and tr_H2R940_H2R940_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QGP7_G3QGP7_GORGO_9595 and sp_Q5T447_HECD3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_F6SGJ7_F6SGJ7_HORSE_9796 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_F1SAD7_F1SAD7_PIG_9823 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_G1L854_G1L854_AILME_9646 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_F1MYD0_F1MYD0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A2U4B8G1_A0A2U4B8G1_TURTR_9739 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A2U3WJA3_A0A2U3WJA3_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A2Y9K7A9_A0A2Y9K7A9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A2Y9NNF1_A0A2Y9NNF1_DELLE_9749 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A2Y9T1X5_A0A2Y9T1X5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A384CL07_A0A384CL07_URSMA_29073 are exactly identical! WARNING: Sequences tr_E2R1V2_E2R1V2_CANLF_9615 and tr_A0A384ABL1_A0A384ABL1_BALAS_310752 are exactly identical! WARNING: Sequences tr_H0W0H3_H0W0H3_CAVPO_10141 and tr_G5BET4_G5BET4_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A1D5QC42_A0A1D5QC42_MACMU_9544 and tr_A0A0D9RLA1_A0A0D9RLA1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HR90_F7HR90_MACMU_9544 and tr_A0A096MST9_A0A096MST9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HR90_F7HR90_MACMU_9544 and tr_A0A2K5NLE0_A0A2K5NLE0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HR90_F7HR90_MACMU_9544 and tr_A0A2K5YD99_A0A2K5YD99_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091JWT9_A0A091JWT9_EGRGA_188379 and tr_A0A0A0AGI3_A0A0A0AGI3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1S3NBG8_A0A1S3NBG8_SALSA_8030 and tr_A0A060XST7_A0A060XST7_ONCMY_8022 are exactly identical! WARNING: Duplicate sequences found: 45 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.reduced.phy Alignment comprises 1 partitions and 1698 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1698 Gaps: 46.77 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/3_mltree/Q14999.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 425 / 34000 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -261236.542947 [00:00:00 -261236.542947] Initial branch length optimization [00:00:03 -258225.491511] Model parameter optimization (eps = 0.100000) [00:01:51] Tree #1, final logLikelihood: -256545.071769 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.194839,0.804199) (0.088016,1.456486) (0.433958,0.705973) (0.283186,1.443408) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14999/4_raxmlng_ancestral/Q14999.raxml.log Analysis started: 02-Jun-2021 18:26:31 / finished: 02-Jun-2021 18:28:34 Elapsed time: 122.368 seconds Consumed energy: 8.593 Wh